| scholarly article | Q13442814 |
| P6179 | Dimensions Publication ID | 1046243054 |
| P356 | DOI | 10.1038/NRG3242 |
| P2888 | exact match | https://scigraph.springernature.com/pub.10.1038/nrg3242 |
| P932 | PMC publication ID | 3541939 |
| P698 | PubMed publication ID | 22705667 |
| P50 | author | Ross Hardison | Q27063030 |
| James Taylor | Q30362443 | ||
| P2860 | cites work | Identification of regulatory regions which confer muscle-specific gene expression. | Q52242949 |
| Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. | Q52250231 | ||
| Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome | Q63433341 | ||
| The SV40 enhancer can be dissected into multiple segments, each with a different cell type specificity | Q69816464 | ||
| Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project | Q21061203 | ||
| A user's guide to the encyclopedia of DNA elements (ENCODE) | Q21092716 | ||
| Highly conserved non-coding sequences are associated with vertebrate development | Q21092819 | ||
| Functional evolution of a cis-regulatory module | Q21563626 | ||
| Transcriptional Regulatory Elements in the Human Genome | Q22065387 | ||
| Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons | Q22065547 | ||
| Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding | Q22065896 | ||
| Potential etiologic and functional implications of genome-wide association loci for human diseases and traits | Q22066284 | ||
| Evolution of genes and genomes on the Drosophila phylogeny | Q22122220 | ||
| Genome sequence of the Brown Norway rat yields insights into mammalian evolution | Q22122498 | ||
| Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome | Q24530466 | ||
| Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo | Q24530508 | ||
| Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter | Q24564607 | ||
| High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells | Q24614543 | ||
| CTCF: master weaver of the genome | Q24621388 | ||
| Epigenetic priors for identifying active transcription factor binding sites | Q24623379 | ||
| Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals | Q24630840 | ||
| Ultraconservation identifies a small subset of extremely constrained developmental enhancers | Q24648269 | ||
| Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome | Q24648552 | ||
| Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila | Q24796663 | ||
| Transcriptional control in the segmentation gene network of Drosophila | Q24803742 | ||
| Genome-wide location and function of DNA binding proteins | Q28131765 | ||
| Comprehensive mapping of long-range interactions reveals folding principles of the human genome | Q28131819 | ||
| Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome | Q28131828 | ||
| Evolution at two levels in humans and chimpanzees | Q28141105 | ||
| The protein CTCF is required for the enhancer blocking activity of vertebrate insulators | Q28142800 | ||
| A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly | Q28184095 | ||
| ChIP-seq accurately predicts tissue-specific activity of enhancers | Q28235102 | ||
| Histone modifications at human enhancers reflect global cell-type-specific gene expression | Q28238467 | ||
| Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression | Q28263560 | ||
| A conserved sequence in the immunoglobulin J kappa-C kappa intron: possible enhancer element | Q28265466 | ||
| Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy | Q28265885 | ||
| High-resolution mapping and characterization of open chromatin across the genome | Q28266995 | ||
| ChIP-Seq identification of weakly conserved heart enhancers | Q28291198 | ||
| Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project | Q28301622 | ||
| Next-generation genomics: an integrative approach | Q28730711 | ||
| 28-way vertebrate alignment and conservation track in the UCSC Genome Browser | Q28756596 | ||
| Genome-wide mapping of in vivo protein-DNA interactions | Q29547162 | ||
| Mapping and analysis of chromatin state dynamics in nine human cell types | Q29547552 | ||
| The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae | Q29614854 | ||
| Population genomics of human gene expression | Q29614905 | ||
| Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation | Q29615949 | ||
| In vivo enhancer analysis of human conserved non-coding sequences | Q29616554 | ||
| Epigenetics: a landscape takes shape | Q29616623 | ||
| Genome-wide analysis of mammalian promoter architecture and evolution | Q29616717 | ||
| Identification of functional elements and regulatory circuits by Drosophila modENCODE | Q29617551 | ||
| Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing | Q29618021 | ||
| Gene regulatory networks and the evolution of animal body plans | Q29618587 | ||
| Diversity and complexity in DNA recognition by transcription factors | Q29619632 | ||
| The NIH Roadmap Epigenomics Mapping Consortium | Q29619856 | ||
| Detection of nonneutral substitution rates on mammalian phylogenies | Q30080028 | ||
| SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation. | Q30702540 | ||
| Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures | Q34712340 | ||
| A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression | Q35001653 | ||
| MEME-ChIP: motif analysis of large DNA datasets | Q35019674 | ||
| Cross-species sequence comparisons: a review of methods and available resources | Q35023949 | ||
| Comprehensive analysis of the chromatin landscape in Drosophila melanogaster | Q35030499 | ||
| Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration | Q35451782 | ||
| Applied bioinformatics for the identification of regulatory elements | Q35766840 | ||
| Comparative genomics at the vertebrate extremes | Q35778678 | ||
| rVista for comparative sequence-based discovery of functional transcription factor binding sites | Q35784206 | ||
| Unsupervised pattern discovery in human chromatin structure through genomic segmentation | Q35923331 | ||
| Conserved non-genic sequences - an unexpected feature of mammalian genomes | Q36045183 | ||
| Reliable prediction of regulator targets using 12 Drosophila genomes | Q36177431 | ||
| USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier | Q36315893 | ||
| We gather together: insulators and genome organization | Q36407771 | ||
| Myc versus USF: discrimination at the cad gene is determined by core promoter elements | Q36568034 | ||
| Chromatin insulators | Q36585889 | ||
| Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus | Q36804854 | ||
| Simian Virus 40 Early- and Late-Region Promoter Functions Are Enhanced by the 72-Base-Pair Repeat Inserted at Distant Locations and Inverted Orientations | Q36939517 | ||
| Sequence census methods for functional genomics | Q37047820 | ||
| Genome-wide approaches to studying chromatin modifications | Q37077306 | ||
| Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells | Q37105909 | ||
| Global mapping of protein-DNA interactions in vivo by digital genomic footprinting | Q37157318 | ||
| Conservation of core gene expression in vertebrate tissues | Q37209981 | ||
| Functional enhancers at the gene-poor 8q24 cancer-linked locus. | Q37279616 | ||
| Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. | Q37467344 | ||
| CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling | Q37484343 | ||
| Genomics of long-range regulatory elements | Q37741229 | ||
| Dynamic GATA factor interplay at a multicomponent regulatory region of the GATA-2 locus | Q38335220 | ||
| Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. | Q38344633 | ||
| 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response | Q39048288 | ||
| Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. | Q39649034 | ||
| Regulation of inducible and tissue-specific gene expression | Q39656942 | ||
| Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model | Q39860941 | ||
| Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors | Q39890524 | ||
| Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. | Q39935609 | ||
| Experimental validation of predicted mammalian erythroid cis-regulatory modules | Q39983560 | ||
| ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements | Q39983825 | ||
| Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus | Q40017617 | ||
| Comparative analysis of the locus control region of the rabbit beta-like gene cluster: HS3 increases transient expression of an embryonic epsilon-globin gene | Q40405841 | ||
| Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance | Q40607315 | ||
| Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional | Q40622576 | ||
| Tissue-specific transcriptional regulation has diverged significantly between human and mouse | Q41833705 | ||
| Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression | Q41995414 | ||
| The SV40 enhancer contains two distinct levels of organization | Q42117036 | ||
| Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse | Q42594046 | ||
| The phylogenetic distribution of non-CTCF insulator proteins is limited to insects and reveals that BEAF-32 is Drosophila lineage specific | Q44721718 | ||
| The statistical significance of nucleotide position-weight matrix matches. | Q47323515 | ||
| A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene. | Q48397674 | ||
| Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer. | Q50748616 | ||
| Genome-wide identification of cis-regulatory sequences controlling blood and endothelial development. | Q50780873 | ||
| The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. | Q51565310 | ||
| Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins. | Q52196730 | ||
| MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules | Q30837902 | ||
| Statistical significance of cis-regulatory modules | Q33269955 | ||
| Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data | Q33287630 | ||
| Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes | Q33339100 | ||
| Analysis of combinatorial cis-regulation in synthetic and genomic promoters | Q33386730 | ||
| Genome-wide discovery of human heart enhancers | Q33523952 | ||
| Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers | Q33549139 | ||
| Genome-wide views of chromatin structure | Q33611702 | ||
| A map of open chromatin in human pancreatic islets | Q33687905 | ||
| Assessing computational methods of cis-regulatory module prediction | Q33769725 | ||
| Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs | Q33780964 | ||
| An erythroid-specific, developmental-stage-independent enhancer far upstream of the human "beta-like globin" genes | Q33849519 | ||
| Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping | Q33915748 | ||
| Conserved noncoding sequences are reliable guides to regulatory elements. | Q33916564 | ||
| Sequence features that drive human promoter function and tissue specificity | Q33940927 | ||
| Expression of a β-globin gene is enhanced by remote SV40 DNA sequences | Q34055192 | ||
| Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes | Q34055544 | ||
| Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities | Q34067751 | ||
| Nucleosome dynamics define transcriptional enhancers | Q34099759 | ||
| Variation in transcription factor binding among humans | Q34105133 | ||
| Genomic strategies to identify mammalian regulatory sequences | Q34185992 | ||
| Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution | Q34239260 | ||
| Metazoan promoters: emerging characteristics and insights into transcriptional regulation | Q34258857 | ||
| Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences | Q34327872 | ||
| Genetics of human gene expression: mapping DNA variants that influence gene expression | Q34339168 | ||
| A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila | Q34352447 | ||
| The eve stripe 2 enhancer employs multiple modes of transcriptional synergy | Q34371968 | ||
| Identification and functional analysis of human transcriptional promoters | Q34374098 | ||
| Insulators: many functions, many mechanisms. | Q34515901 | ||
| Methods for calculating the probabilities of finding patterns in sequences | Q34527638 | ||
| Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques | Q34575437 | ||
| Mapping networks of physical interactions between genomic elements using 5C technology | Q34578862 | ||
| DNA motifs in human and mouse proximal promoters predict tissue-specific expression | Q34597423 | ||
| P433 | issue | 7 | |
| P304 | page(s) | 469-483 | |
| P577 | publication date | 2012-06-18 | |
| P1433 | published in | Nature Reviews Genetics | Q1071824 |
| P1476 | title | Genomic approaches towards finding cis-regulatory modules in animals | |
| P478 | volume | 13 |
| Q34001586 | A bioinformatic and computational study of myosin phosphatase subunit diversity |
| Q34700119 | A comparative encyclopedia of DNA elements in the mouse genome |
| Q38614510 | A gene-specific non-enhancer sequence is critical for expression from the promoter of the small heat shock protein gene αB-crystallin |
| Q35904489 | A method to predict the impact of regulatory variants from DNA sequence |
| Q34042831 | Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer |
| Q41877697 | An Enhancer's Length and Composition Are Shaped by Its Regulatory Task |
| Q36703674 | An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability. |
| Q90050931 | An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis |
| Q34575705 | Analysis of the ABCA4 genomic locus in Stargardt disease |
| Q30749750 | Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data |
| Q47321713 | Bioinformatics approaches to predict target genes from transcription factor binding data |
| Q64212113 | Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges |
| Q37638159 | Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations |
| Q37025453 | Chromatin structure and gene regulation: a dynamic view of enhancer function |
| Q26824645 | Combining genomic and proteomic approaches for epigenetics research |
| Q36294386 | Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies. |
| Q38946044 | Comparative FAIRE-seq analysis reveals distinguishing features of the chromatin structure of ground state- and primed-pluripotent cells |
| Q36426366 | Complex inheritance of ABCA4 disease: four mutations in a family with multiple macular phenotypes |
| Q38429205 | Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia |
| Q40613576 | DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements |
| Q34695037 | De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets |
| Q46124101 | Detecting clustering and ordering binding patterns among transcription factors via point process models |
| Q42379627 | Discovering enhancers directly by activity |
| Q33839426 | Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. |
| Q38862967 | Dynamic Gene Regulatory Networks of Human Myeloid Differentiation |
| Q35068557 | Dynamic regulation of transcriptional states by chromatin and transcription factors. |
| Q38168524 | Embryonic Stem Cells: A Perfect Tool for Studying Mammalian Transcriptional Enhancers |
| Q28084490 | Emerging applications of read profiles towards the functional annotation of the genome |
| Q26782747 | Enabling functional genomics with genome engineering |
| Q26860795 | Epigenetic mechanisms and developmental choice hierarchies in T-lymphocyte development |
| Q38233723 | Epigenetic pathway targets for the treatment of disease: accelerating progress in the development of pharmacological tools: IUPHAR Review 11. |
| Q34034627 | Evolution of hemoglobin and its genes |
| Q35128053 | FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells |
| Q36929482 | From remote enhancers to gene regulation: charting the genome's regulatory landscapes |
| Q27002416 | From trans to cis: transcriptional regulatory networks in neocortical development |
| Q42292926 | Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. |
| Q47995230 | Functional evolution of cis-regulatory modules of STMADS11 superclade MADS-box genes |
| Q38163235 | Fundamentals of vitamin D hormone-regulated gene expression |
| Q48227104 | Gains and Losses of Cis-regulatory Elements Led to Divergence of the Arabidopsis APETALA1 and CAULIFLOWER Duplicate Genes in the Time, Space, and Level of Expression and Regulation of One Paralog by the Other. |
| Q42800050 | Genome-wide characterization of mammalian promoters with distal enhancer functions |
| Q35097288 | Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution |
| Q57156960 | Genome-wide identification of enhancer elements in the placenta |
| Q36084287 | Genomic approaches for understanding the genetics of complex disease |
| Q85373276 | High throughput technologies for the functional discovery of mammalian enhancers: new approaches for understanding transcriptional regulatory network dynamics |
| Q34043754 | High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. |
| Q50126824 | Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. |
| Q47278823 | Identification of H3K4me1-associated proteins at mammalian enhancers |
| Q37091618 | Identification of HMX1 target genes: a predictive promoter model approach |
| Q30441416 | Identification of biologically relevant enhancers in human erythroid cells |
| Q35020329 | Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library. |
| Q38650325 | Identification of three new cis-regulatory IRF5 polymorphisms: in vitro studies. |
| Q35117066 | Identifying transcriptional cis-regulatory modules in animal genomes. |
| Q33698455 | Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. |
| Q49407511 | Incorporation of a skeletal muscle-specific enhancer in the regulatory region of Igf1 upregulates IGF1 expression and induces skeletal muscle hypertrophy. |
| Q38310745 | Indirect p53-dependent transcriptional repression of Survivin, CDC25C, and PLK1 genes requires the cyclin-dependent kinase inhibitor p21/CDKN1A and CDE/CHR promoter sites binding the DREAM complex |
| Q35740799 | Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera |
| Q35465289 | Loregic: a method to characterize the cooperative logic of regulatory factors |
| Q34556377 | Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation |
| Q38882162 | Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility |
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| Q33784387 | Molecular hyperdiversity and evolution in very large populations |
| Q30574547 | MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data |
| Q35176534 | Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways |
| Q37236835 | Multiple alignment-free sequence comparison |
| Q35608650 | Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility |
| Q50694000 | Otx2 expression in anterior neuroectoderm and forebrain/midbrain is directed by more than six enhancers. |
| Q35857834 | PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information |
| Q38704636 | Post-GWAS methodologies for localisation of functional non-coding variants: ANGPTL3. |
| Q92217592 | Primate optogenetics: Progress and prognosis |
| Q28084330 | Protein-DNA binding in high-resolution |
| Q44357084 | Protein-mRNA interactome capture: cartography of the mRNP landscape |
| Q33877534 | Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits. |
| Q36135823 | SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules |
| Q35022394 | Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA |
| Q37697916 | Sequence signatures extracted from proximal promoters can be used to predict distal enhancers |
| Q37127728 | Strategies for targeting primate neural circuits with viral vectors |
| Q38102648 | Structural variations, the regulatory landscape of the genome and their alteration in human disease |
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| Q34066130 | Technical considerations for functional sequencing assays |
| Q41437245 | The Role of Epigenetics in Type 1 Diabetes |
| Q33720405 | The Role of the Molecular Clock in Skeletal Muscle and What It Is Teaching Us About Muscle-Bone Crosstalk. |
| Q39945896 | The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification |
| Q42370747 | The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies |
| Q37012934 | The impact of trans-regulation on the evolutionary rates of metazoan proteins |
| Q33891792 | Three members of Medicago truncatula ST family are ubiquitous during development and modulated by nutritional status (MtST1) and dehydration (MtST2 and MtST3). |
| Q34379841 | Topology of mammalian developmental enhancers and their regulatory landscapes |
| Q55323106 | Towards a map of cis-regulatory sequences in the human genome. |
| Q28067751 | Transcriptional Dynamics at Brain Enhancers: from Functional Specialization to Neurodegeneration |
| Q34631682 | Transcriptional and epigenetic regulation of T-helper lineage specification |
| Q39042849 | Transcriptional architecture of the mammalian circadian clock |
| Q38194866 | Transcriptional enhancers: from properties to genome-wide predictions |
| Q36263009 | Unrealistic phylogenetic trees may improve phylogenetic footprinting |
| Q26865379 | Using the ENCODE Resource for Functional Annotation of Genetic Variants |
| Q35251388 | We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects. |
| Q34914419 | cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila |
| Q30980309 | groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data |
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